All my favorites, though you've probably seen them already:

A Better Whiterun - City Under Construction

http://skyrim.nexusmods.com/downloads/file.php?id=15776

Apocalypse Spell Package

http://skyrim.nexusmods.com/downloads/file.php?id=16225

Cloaks of Skyrim

http://skyrim.nexusmods.com/downloads/file.php?id=12092

Deadly Dragons

http://skyrim.nexusmods.com/downloads/file.php?id=3829

Dragon Falls Manor

http://skyrim.nexusmods.com/downloads/file.php?id=10901

Flyable Dragon Races --Flying Mod- BtD2-- (In my opinion better than other dragon mods)

http://skyrim.nexusmods.com/downloads/file.php?id=16532

JaySuS Swords

http://skyrim.nexusmods.com/downloads/file.php?id=1002

Midas Magic

http://skyrim.nexusmods.com/downloads/file.php?id=3413

Millenia Weapon Retexture Project - WRP

http://skyrim.nexusmods.com/downloads/file.php?id=1754

Skyrim HD - 2K Textures (Better than the HD DLC)

http://skyrim.nexusmods.com/downloads/file.php?id=607

SkyUI (a must)

http://skyrim.nexusmods.com/downloads/file.php?id=3863

Static Mesh Improvement Mod - SMIM

http://skyrim.nexusmods.com/downloads/file.php?id=8655

Tales of Lycanthropy - Werewolf Overhaul

http://skyrim.nexusmods.com/downloads/file.php?id=12687

Better Vampires by Brehanin 4_0

http://skyrim.nexusmods.com/downloads/file.php?id=9717

Weapons of the Third Era

http://skyrim.nexusmods.com/downloads/file.php?id=3871

XCE - Xenius Character Enhancement

http://skyrim.nexusmods.com/downloads/file.php?id=2356